Fig. 2

Genome-wide identification of candidate genes with locally restricted expression in stage-3 embryo. A Outline of the experimental procedure. B Images showing live stage-3 embryos following isolation of cells from 3 different regions (yellow arrowheads; central [c], intermediate [i], and peripheral [p]) of the embryo, along with the schematic showing the isolated cells used for RNA-seq. Scale bar, 100 µm. C–E Three types of comparison using RNA-seq datasets from the c, i, and p cells (comparison I: c cells versus i/p cells [C]; comparison II: p cells versus c/i cells [D]; comparison III: i cells versus c/p cells [E]) detected candidates of differentially expressed genes (DEGs). Top: schematic showing the grouping of the datasets for comparison. Middle: MA-plot of log₂ fold-change (FC) versus log₂ average expression level (CPM; count per million) from 10,862 genes. Bottom: lists of DEG candidates with normalized expression levels (CPM) from biological replicates of the three sample types (c1, c2, i1, i2, i3, p1, p2, and p3), which are sorted by FDR values. Genes with FDR < 0.05 are highlighted in red, and candidates of DEGs that were selected for a pilot pRNAi screen are indicated by plus signs in the MA-plots and tables. Each table displays the top 35 genes; the full lists are presented in Additional file 2: Tables S1–S3. Note that genes marked by asterisks appear in multiple tables